Publications 2022

Journal Articles          Review Articles          Book Chapters          Preprints


Journal articles


Pneumolysin promotes host cell necroptosis and bacterial competence during pneumococcal meningitis as shown by whole-animal dual RNA-seq

Authors: Jim, KK., Aprianto, R., Koning, R., Domenech, A., Kurushima, J., van de Beek, D., Vandenbroucke-Grauls CMJE., Bitter, W., and Veening, J.W.

Published in:  Cell Reports 2022 Vol. 41

DOI: 10.1016/j.celrep.2022.111851


Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications

Authors: Malinovska, L., Cappelletti, V., Kohler, D., Piazza, I., Tsai, T.H., Pepelnjak, M., Stalder, P., Dörig, C., Sesterhenn, F., Elsässer, F., Kralickova, L., Beaton, N., Reiter, L., de Souza, N., Vitek, O., and Picotti, P.

Published in:  Nature Protocols 2022

DOI: 10.1038/s41596-022-00771-x


Mechanism of cyclic β-glucan export by ABC transporter Cgt of Brucella

Authors: Sedzicki, J., Ni, D., Lehmann, F., Wu, N., Zenobi, R., Jung, S., Stahlberg, H.,* and Dehio, C.*

Published in: Nature Structural & Molecular Biology 2022 Vol. 29

DOI: 10.1038/s41594-022-00868-7


Shared biophysical mechanisms determine early biofilm architecture development across different bacterial species

Authors: Jeckel, H.*, Díaz-Pascual, F.*, Skinner, DJ.*, Song, B.*, Jiménez-Siebert, E., Strenger, K., Jelli, E., Vaidya, S., Dunkel, J.,* and Drescher, K.*

Published in: PLoS Biology 2022

DOI: 10.1371/journal.pbio.3001846


2FAST2Q: a general-purpose sequence search and counting program for FASTQ files

Authors: Bravo, AM., Typas, A., and Veening J.W.

Published in: PeerJ 2022

DOI: 10.7717/peerj.14041


Antibiotic polymyxin arranges lipopolysaccharide into crystalline structures to solidify the bacterial membrane

Authors: Manioglu, S., Modaresi, S.M., Ritzmann, N., Thoma, J., Overall, S.A., Harms, A., Upert, G., Luther, A., Barnes, A.B., Obrecht, D., Müller, D.J.*, and Hiller, S.*

Published in: Nature Communications 2022 Vol. 13

DOI: 10.1038/s41467-022-33838-0


reComBat: batch-effect removal in large-scale multi-source gene-expression data integration

Authors: Adamer, M.F.*, Brüningk, S.C.*, Tejada-Arranz, A., Estermann, F., Basler, M., and Borgward, K.

Published in: Bioinformatics Advances 

DOI: 10.1093/bioadv/vbac071


Computational identification of a systemic antibiotic for gram-negative bacteria

Authors: Miller, R.D.*, Iinishi, A.*, Modaresi, S.M.*, Yoo, B.K.*, Curtis, T.D., Lariviere, P.J., Liang, L., Son, S., Nicolau, S., Bargabos, R., Morrissette, M., Gates, M.F., Pitt, N., Jakob, R.P., Rath, P., Maier, T., Mayutin, A.G., Kaiser, J.T., Niles, S., Karavas, B., Ghiglieri, M., Bowman, S., Rees, D.C., Hiller, S.*, and Lewis, K.*

Published in: Nature Microbiology 2022 Vol. 7, 1661-1672

DOI: 10.1038/s41564-022-01227-4

Free access to the paper: https://www.ncbi.nlm.nih.gov »


Antibiotic persistence of intracellular Brucella abortus

Authors: Mode, S.*, Ketterer, M.*, Québatte, M.*, and Dehio, C.

Published in: PLoS Negl Trop Dis. 2022

DOI: 10.1371/journal.pntd.0010635


The acquisition of clinically relevant amoxicillin resistance in Streptococcus pneumoniae requires ordered horizontal gene transfer of four loci

Authors: Gibson, P.S., Bexkens, E., Zuber, S., Cowley, L.A. , and Veening, J.W.

Published in: PLOS Pathogens 2022

DOI: 10.1371/journal.ppat.1010727


Amoxicillin-resistant Streptococcus pneumoniae can be resensitized by targeting the mevalonate pathway as indicated by sCRilecs-seq

Authors: Dewachter, L., Dénéréaz, J., Liu, X., de Bakker, V., Costa, C., Baldry, M., Sirard, J.C., and Veening, J.W.

Published in: eLife 2022 Vol. 11

DOI: 10.7554/eLife.75607


Combining CRISPRi and metabolomics for functional annotation of compound libraries

Authors: Anglada-Girotto, M., Handschin, G., Ortmayr, K., Campos, A.I., Gillet, L., Manfredi, P., Mulholland, C.V., Berney, M., Jenal, U., Picotti, P., and Zampieri, M.

Published in: Nature Chemical Biology 2022 Vol. 18

DOI: 10.1038/s41589-022-00970-3

Free access to the paper: https://edoc.unibas.ch »


CRISPRi-seq for genome-wide fitness quantification in bacteria

Authors: de Bakker, V.*, Liu, X.*, Bravo, A.M., and Veening, J.W.

Published in: Nature Protocols 2022 Vol. 17 Issue 2

DOI: 10.1038/s41596-021-00639-6

Free access to the paper: https://docs.google.com/ »


Review articles


Toothpicks, logic, and next-generation sequencing: systematic investigation of bacteriophage-host interactions

Authors: Shaidullina, A. and Harms, A.

Published in: Current Opinion in Microbiology Vol. 70

DOI: 10.1016/j.mib.2022.102225


Circuit-Based Design of Microfluidic Drop Networks

Authors: Rousset, N., Lohasz, C., Boos, J.A., Misun, P.M., Cardes, F., and Hierlemann, A.

Published in: Micromachines 2022 Vol. 13 Issue 7

DOI: 10.3390/mi13071124


INCATE: a partnership to boost the antibiotic pipeline

Comment

Authors: Alt, S., Haggstrom, D., Kessmann, H., Kloss, F., Schneider, C.E., Jäger, T., Schwede, T., Brakhage, A., and Dehio, C.

Published in: Nature Reviews Drug Discovery 2022

DOI: 10.1038/d41573-022-00138-7

Free access to the article: https://edoc.unibas.ch/ »


Mechanisms Underlying Vibrio cholerae Biofilm Formation and Dispersion

Authors: Teschler, J.K., Nadell, C.D., Drescher, K., and Yildiz, F.H.

Published in: Annual Review of Microbiology 2022 Vol. 76

DOI: 10.1146/annurev-micro-111021-053553


Expanding the search for small-molecule antibacterials by multidimensional profiling

Authors: Ortmayr, K., de la Cruz Moreno, R., and Zampieri, M.

Published in: Nature Chemical Biology 2022 Vol. 18

DOI: 10.1038/s41589-022-01040-4

Free access to the article: https://edoc.unibas.ch »


Book chapters


Limited Proteolysis–Mass Spectrometry to Identify Metabolite–Protein Interactions.

Authors: Holfeld, A., Quast, J.P., Bruderer, R., Reiter, L., de Souza, N., and Picotti, P.

Published in: Methods in Molecular Biology 2023 Vol. 2554

DOI: 10.1007/978-1-0716-2624-5_6


Preprints


High-content screening identifies a critical role for P pili in early adhesion of uropathogenic Escherichia coli to bladder cells

Authors: Simonet, T., Rutschmann, O., Sharma, K., Nass, T., Pavlou, M., Dubois, A., Knott, G., and McKinney, J.

Preprint: Research Square

Publication date: December 19, 2022 (version 1)

DOI: 10.21203/rs.3.rs-2379019/v1